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Abstrak :
Latar Belakang : Enterococcus faecalis merupakan bakteri yang mampu membentuk biofilm dan banyak ditemukan pada kasus kegagalan perawatan saluran akar. Tujuan : Melihat daya antibakteri kitosan dan klorheksidin terhadap E. faecalis dalam biofilm. Metode : Deteksi dan kuantifikasi E. faecalis dalam biofilm yang hidup pasca pemaparan bahan uji, dengan real time PCR. Hasil : Terdapat perbedaan jumlah bakteri yang signifikan antara kedua kelompok bahan uji terhadap kontrol (p ≤ 0,05), tetapi tidak terdapat perbedaan bermakna antara kelompok kitosan dan klorheksidin. Kesimpulan : Daya antibakteri kitosan 2% terhadap biofilm E. faecalis sebanding dengan klorheksidin 2%. ......Background : Enterococcus faecalis has an ability to form biofilms and become a predominant bacteria that plays a major role in the etiology of persistent lesions after root canal treatment. Aim : To analyze the efficacy of chitosan and chlorhexidine against E. faecalis in biofilms. Methods : Detection and quantification of E. faecalis DNA that survive and live after immersing the biofilm in antibacterial solution, with real time PCR. Result : Statistically there is significant difference of living E. faecalis between chitosan and control and between 2% chlorhexidine and control (p ≤0,05). But there is no significant different between chitosan and chlorhexidine (p>0,05). Conclusion : Antibacterial effectivity of chitosan is equal to chlorhexidine against E. faecalis in biofilm.

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ABSTRAK
Pneumocystis jirovecii adalah penyebab infeksi oportunistik di saluran pernapasan bawah pada individu dengan sistem kekebalan tubuh yang lemah, terutama pada pasien HIV. Pemeriksaan infeksi P.jirovecii di Indonesia masih berdasarkan pemeriksaan klinis dan mikroskopis, yang memerlukan waktu yang cukup lama, kurang sensitif dan spesifik. Karena alasan tersebut dalam penelitian ini dikembangkan uji molekuler real time PCR (rPCR) yang lebih sensitif dan spesifik. Uji rPCR telah berhasil dioptimasi dengan kemampuan deteksi minimum DNA 6,55 copy/μl dan tidak bereaksi silang dengan mikroorganisme yang diuji pada penelitian ini. Dibandingkan dengan uji mikroskopis, uji rPCR memberikan hasil positif 20% lebih tinggi daripada uji mikroskopis. Uji rPCR dapat mendeteksi P.jirovecii pada sampel klinis sputum dan sputum induksi dari pasien HIV dengan pneumonia dengan jumlah sel CD4+ > 200 maupun ≤ 200. Oleh karena itu, uji rPCR yang telah dioptimasi dalam studi ini dapat mendeteksi P.jirovecii pada sampel klinis sputum dan sputum induksi dari pasien HIV dengan pneumonia dengan jumlah sel CD4+ > 200 maupun ≤ 200

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ABSTRACT
Pneumocystis jirovecii is the cause of opportunistic infections in the lower respiratory tract in individuals with weakened immune systems, especially in patients with HIV. Examination P.jirovecii infection in Indonesia was based on clinical and microscopic examination, requiring considerable time, less sensitive and specific. Because of these reasons in this study developed a molecular test real time PCR (rPCR) is more sensitive and specific. rPCR test has been successfully optimized with minimum DNA detection capabilities 6.55 copy/μL and do not cross-react with the microorganisms were tested in this study. Compared with microscopic test, test rPCR gives positive result 20% higher than the microscopic test. rPCR test can detect P.jirovecii on clinical samples of sputum and sputum induction of HIV patients with pneumonia with CD4+ cell counts > 200 or ≤ 200. Therefore, rPCR test which has been optimized in this study can detect P.jirovecii in clinical sputum samples and sputum induction of HIV patients with pneumonia with CD4+ cell counts > 200 or ≤ 200

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ABSTRAK
Helicobacter pylori diperkirakan menginfeksi lebih dari setengah populasi orang dewasa. Deteksi dini H.pylori sangat diperlukan untuk mencegah berkembangnya infeksi menjadi keganasan lambung. Bentuk coccoid dari H. pylori sulit dideteksi dengan kultur dan histopatologi, namun dapat terdeteksi dengan metode molekuler seperti real-time PCR. Salah satu gen yang dapat digunakan sebagai gen target real-time PCR yaitu 16S rRNA, yang diketahui spesifik dan juga digunakan untuk menganalisis kekerabatan antar strain. Analisis ini bermanfaat untuk melihat penyebaran infeksi H.pylori di dunia. Penelitian ini merupakan penelitian eksperimental laboratorium. Metode pengambilan sampel yang digunakan yaitu, metode consecutive sampling. Biopsi diambil dari 2 antrum dan 2 korpus pada 42 penderita dispepsia untuk pemeriksaan real-time PCR dan histopatologi. Optimasi kondisi real-time PCR meliputi uji volume cetakan DNA, sensitifitas dan spesifisitas teknik, kemudian dilanjutkan aplikasi pada sampel klinis dari biopsi lambung. Delapan dari 11 sampel yang positif dilakukan sekuensing dan analisis filogenetik. Hasil optimasi diperoleh suhu annealing 64?C, konsentrasi primer 0,8 ?M dan konsentrasi probe 0,6 ?M. Ambang batas deteksi real-time PCR untuk mendeteksi jumlah DNA minimal H.pylori yaitu 46 bakteri. Spesifisitas uji reaksi silang real-time PCR ini tidak menunjukkan adanya reaksi silang dengan mikroorganisme lain. Proporsi positif hasil pemeriksaan real-time PCR sebesar 26,2 , sedangkan histopatologi sebesar 11,9 . Pemeriksaan real-time PCR mampu meningkatkan diagnosis sebesar 14,3 dibandingkan pemeriksaan histopatologi. Hasil sekuensing dan analisis filogenetik menunjukkan bahwa strain H.pylori dari sampel memiliki kekerabatan dengan strain Taiwan, India, dan Australia. Kata kunci : H.pylori, histopatologi, real-time PCR, analisis filogenetik

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ABSTRACT
Helicobacter pylori infection is estimated infect almost half of the adult population in the world. Early detection of H.pylori is needed to prevent the development of infections into gastric malignancies. The coccoid form of H. pylori is difficult to detect using culture and histopathology but it can be detected by molecular methods such as real time PCR. One of the genes that can be used as a real time PCR target gene is 16S rRNA, which is known to be specific and also used to analyze closely related strain. This analysis were useful to showed the spread of H.pylori infection in the world.This study is an experimental laboratory. The sampling method used is the consecutive sampling method. Biopsy was taken from 2 antrum and 2 corpus in 42 patients with dyspepsia for real time PCR and histopathology examination. Optimization real time PCR conditions include DNA template volume testing, sensitivity and specificity of the technique, followed by application of clinical samples from gastric biopsy. Eight of the 11 positive samples were sequenced and analyzed for phylogenetics pattern. The optimization result obtained annealing temperature 64 C, primer concentration was 0,8 M and probe concentration was 0,6 M. Limit detection of the DNA was 46 bacteria. The specificity of the PCR 39 s real time indicate that there was no cross reaction with other microorganisms. The positive proportion of PCR real time examination was 26.2 , while histopathology was 11.9 . A real time PCR examination was able to improve the diagnosis by 14,3 compared to histopathology examination. Sequencing and phylogenetic analysis results showed that our strain were closely related to Taiwan, India and Australia strains. Keywords H.pylori, histopathology, real time PCR, phylogenetic analysis

Abstrak :
Uveitis jarang terjadi dengan insidens sekitar 52/100.000 penduduk/tahun namun dapat mengakibatkan kebutaan. Diagnosis uveitis di Indonesia selama ini berdasarkan gambaran klinis dan belum dibuktikan dengan pemeriksaan deteksi mikroba sehingga belum diketahui prevalensi patogen uveitis. Penelitian ini bertujuan untuk meningkatkan peran uji real time PCR sebagai pendukung diagnosis etiologi sehingga dapat diketahui proporsi Mycobacterium tuberculosis, Toxoplasma gondii, Rubella, Herpes simplex, Varicella zoster, Epstein barr, Cytomegalovirus sebagai penyebab uveitis dan analisis kesesuaian diagnosis klinis dengan hasil pemeriksaan real time PCR. Pengambilan sampel cairan akuos dilakukan di Departemen Ilmu Kesehatan Mata FKUI-RSCM, sedangkan untuk uji real time PCR dilakukan di Laboratorium Mikrobiologi Klinik FKUI-RSCM selama rentang waktu Oktober 2016 sampai Mei 2017. Terdapat total 81 pasien dengan diagnosis klinis uveitis infeksi 32, 22 uveitis non-infeksi, dan 27 idiopatik. Berdasarkan uji real time PCR diperoleh hasil bahwa patogen terbanyak yaitu CMV diikuti oleh Toxoplasma Gondii dan Mycobacterium tuberculosis. Mikroba terdeteksi pada 14 spesimen diantara 32 uveitis infeksi, 1 spesimen diantara 22 uveitis non-infeksi, dan 2 diantara 27 uveitis idopatik. Dari 17 hasil positif real time PCR 13 sampel menunjukkan hasil PCR yang sesuai dengan klinis sedangkan 4 sampel tidak sesuai. Deteksi mikroba menggunakan pemeriksaan PCR pada cairan akuos dapat membantu dalam penegakan diagnosis dan tatalaksana uveitis dengan tepat.

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Uveitis is a rare disease with an incidence of 52 100,000 population year but can cause blindness. The diagnosis of uveitis in Indonesia has been upheld primarily based on clinical features and has not been proven by microbial detection, so it is never known precisely the prevalence of uveitis pathogens. This study aims to increase the role of microbiological examination of real time PCR as supporting the etiology diagnosis so that it can be known the proportion of Mycobacterium tuberculosis, Toxoplasma gondii, Rubella, Herpes simplex, Varicella zoster, Epstein barr, Cytomegalovirus as cause of uveitis and assess a clinical diagnosis accordance with real time PCR results. Aqueous tap was conducted at the Department of Opthalmology FMUI RSCM, while for real time PCR was conducted at Clinical Microbiology Laboratory FMUI RSCM during October 2016 until May 2017. There were a total of 81 patients with clinical diagnosis consisting of 32 infectious uveitis, 22 non infectious uveitis, and 27 idiopathic uveitis. Based on real time PCR results obtained that the most common pathogens are CMV followed by Toxoplasma Gondii and Mycobacterium tuberculosis. Microbes were detected in 14 specimens among 32 infectious uveitis, 1 sample among 22 non infectious uveitis, and 2 of 27 idiopathic uveitis. Out of 17 positive results of real time PCR 13 samples showed a clinically accordance with the real time PCR result whereas 4 samples did not. Microbial detection using PCR of aqueous humor is helpful in diagnosing and management of uveitis.

Abstrak :
Leptospirosis adalah penyakit infeksi akut yang dapat menyerang rnanusia maupun hewan yang disebabkan bakteri Leprospfra spp dan digolongkan sebagai zoonosis. Gejala klinis leptospirosis yang tidak spesiiik dan sulitnya uji laboratorium untuk konfirmasi diagnosis mengakibatkan penyakit ini seringkali tidak terdiagnosis. Oleh karena itu dalam ponelirian ini dilakukan optimasi uji diagnostik molekuler menggimakan real-time PCR sebagai deteksi cepat, sensitif dan spesiflk untuk Leptospira patogen pada manusia DNA bakten di dalam spesimen darah diekstraksi menggunak:an QIAamp DNA Blood Mini Kit, Qiagen dan spesimen urin diekstraksi menggunakan QIAamp DNA Stool Mini Kit,Qiagen dengan prosodur sesuai dengan petunjuk manualnya. Primer dan probe yang digunakan berdasarkan publikasi penelitian oleh Smythe dkk, 2002. Dari hasil uji optimasi kondisi optimal real-time PCR didapat suhu annealing 60°c, konsentrasi primer 0,9 uM dan konsentrmi probe 0,2 uM. Spesifisitas primer diuji menggunakan DNA balcteri patogen lain Hasii uji sensitiiitas real-time PCR untuk mendeteksi konsentrasi DNA terendah bakteri Leprospim spp adalah 0,75 fypl, hasil uji spesitisitas real-time PCR menunjukkan bahwa primer yang digunakan untuk deteksi balderi Leprospira spp tidak beraksi silang dengan genom bakteri-bakteri uji, konsentrasi minimal DNA bakteri yang masih terdeteksi dalam darah mencapai 150 fg/pl, sedangkan dalam urin mencapai 1470 fg/pl yang masih dapat dideteksi dengan pemeriksaan real-time PCR. Metode real-time PCR ini dapat digunakan sebagai alternatif pemeriksaan mikrobiologi yang cepat dan tepat untuk mendiagnosis leptospirosis. ......Leptospirosis is an emerging infectious disease in human and animals caused by Leptospira spp. and considered endemic in Indonesia due to its tropical climate. The International Leptospirosis Society (2001) declared Indonesia has high incidence of leptospirosis and ranked the third in the world for mortality (16.7%) The clinical features are not specific and may result in a missed or delayed diagnosis. The microbiology diagnostic method e.g. culture and microscopic agglutination test (MAT) are sensitive and specific but time-consuming and high cost. The other method to detect the antibody result false positive reactions and need confirmation by the MAT. Therefore in this study we optimized the real-time PCR assay, which has been used to detect a large number of microbes. It has high sensitivity and specificity, thus making it ideal as a rapid and accurate method to detect pathogen Leptospira spp. in human specimens. The amplification of the DNA control was performed optimally with the following conditions: annealing temperature is 60°C, primer volume is 0.5p1 (final concentration: 0.9 phd); probe volume is 0.2 ul (final concentration 0.2 pM). This method may detect the DNA in the Mastermix Mix with the concentration of 0.75 fg/ul, however in blood specimen the limit of detection of the DNA 150 fg/pl and in urine is 1470 fg/pl. The primer used in this assay is not complementary with the DNA of other pathogenic Leptospira spp. The real-time PCR assay is a rapid and accurate method to detect pathogenic Leptospira in human specimens. Further studies are needed to know the sensitivity and specificity of the real-time PCR assay compared to other diagnostic methods in clinical settings.

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ABSTRAK
Latar belakang: Diare masih merupakan masalah kesehatan masyarakat di negara berkembang karena morbiditas dan mortalitasnya yang masih tinggi. Diare dapat disebabkan oleh virus, bakteri dan parasit yang penting diketahui untuk memberikan tatalaksana yang tepat, namun saat ini belum ada data mengenai bakteri penyebab diare di Indonesia. Tujuan: Mengetahui gambaran klinis anak dengan diare akut dan mengetahui jenis bakteri enteropatogen penyebab diare akut dengan menggunakan real-time PCR di Rumah Sakit Cipto Mangunkusumo. Metode: Penelitian potong lintang pada anak dengan diare akut berusia 1-15 tahun di Rumah Sakit Cipto Mangunkusumo. Hasil: Subyek penelitian ini terdiri dari 60 subyek dengan diare akut. Sebagian besar berusia 1-3 tahun, status gizi baik, berasal dari ibu dengan pendidikan sedang dengan status ekonomi keluarga menengah rendah, sebagian besar belum mendapat antibiotik sebelum ke rumah sakit tetapi sudah mendapat cairan rehidrasi oral. Gambaran klinis diare akut akibat infeksi bakteri yaitu frekuensi diare ≤5X/hari (p=0,018), tanpa leukositosis feses (p=0,015) dan malabsorpsi lemak (p=0,031). Sebaran infeksi bakteri patogen penyebab diare akut berdasarkan real-time PCR sebagai berikut: Campylobacter jejuni 7 subyek, Escherichia coli patogen 17 subyek yang terdiri dari EPEC 9 subyek, EIEC 5 subyek dan ETEC 3 subyek. Infeksi bakteri campuran pada subyek sebagai berikut: EPEC+EIEC 2 subyek , C.jejuni+EPEC 1 subyek, C.jejuni+EPEC+EIEC 1 subyek dan C.jejuni+EPEC+ETEC 1 subyek. Simpulan: Sebagian besar diare terjadi pada usia 1-3 tahun dengan status pasien gizi baik dengan status keluarga menengah rendah. Sekitar 48% anak dengan diare akut didapatkan bakteri dari hasil real-time PCR feses dengan proporsi terbanyak yaitu EPEC, diikuti Campylobacter jejuni, EIEC dan ETEC. ABSTRACT
Background: Diarrhea is still a public health problem in developing countries due to it?s morbidity and mortality. Diarrhea can be caused by viruses, bacteria and parasites. It is important to know the etiology to provide proper management, but there is currently no data on the bacteria that causes diarrhea in Indonesia. Objective: To characterize the clinical manifestations of children with acute diarrhea and determine the type of enteropathogens bacteria causing acute diarrhea using real-time PCR in Cipto Mangunkusumo Hospital. Methods: This was a cross-sectional study, done in June-November 2015. Stool specimens were collected from patients aged 1-15 years with acute diarrhea and tested for bacterial enteropathogens using real-time PCR. Results: Of the 60 children enrolled, mostly aged 1-3 years, good nutritional status, from low income families and secondary education mothers, most have not received antibiotics prior to hospital admission but had received oral rehydration fluids. The clinical features of acute diarrhea caused by bacterial infection is diarrhea frequency ≤5X / day without fecal leukocytosis and fat malabsorption. From 60 subjects, 29 (48,3%) children excreted bacteria in their feces prooved by real-time PCR. Distribution of pathogenic bacterial infection causes acute diarrhea by real-time PCR as follows: Campylobacter jejuni 7 subjects, pathogenic Escherichia coli 17 subjects which consists of EPEC 9 subjects, EIEC 5 subjects and ETEC 3 subjects. Multiple infections in subjects as follows: EPEC+EIEC 2 subjects, EPEC+C.jejuni 1 subject, C.jejuni+EPEC+EIEC 1 subject and C.jejuni+EPEC+ETEC 1 subject. Conclusions: Most diarrhea occurs at the age of 1-3 years with good nutritional status of patients with low-medium family status. Approximately 48% of children with acute diarrhea excreted bacteria in their feces prooved by real-time PCR stool with the highest proportion is EPEC, followed by Campylobacter jejuni, EIEC and ETEC. ;Background: Diarrhea is still a public health problem in developing countries due to it?s morbidity and mortality. Diarrhea can be caused by viruses, bacteria and parasites. It is important to know the etiology to provide proper management, but there is currently no data on the bacteria that causes diarrhea in Indonesia. Objective: To characterize the clinical manifestations of children with acute diarrhea and determine the type of enteropathogens bacteria causing acute diarrhea using real-time PCR in Cipto Mangunkusumo Hospital. Methods: This was a cross-sectional study, done in June-November 2015. Stool specimens were collected from patients aged 1-15 years with acute diarrhea and tested for bacterial enteropathogens using real-time PCR. Results: Of the 60 children enrolled, mostly aged 1-3 years, good nutritional status, from low income families and secondary education mothers, most have not received antibiotics prior to hospital admission but had received oral rehydration fluids. The clinical features of acute diarrhea caused by bacterial infection is diarrhea frequency ≤5X / day without fecal leukocytosis and fat malabsorption. From 60 subjects, 29 (48,3%) children excreted bacteria in their feces prooved by real-time PCR. Distribution of pathogenic bacterial infection causes acute diarrhea by real-time PCR as follows: Campylobacter jejuni 7 subjects, pathogenic Escherichia coli 17 subjects which consists of EPEC 9 subjects, EIEC 5 subjects and ETEC 3 subjects. Multiple infections in subjects as follows: EPEC+EIEC 2 subjects, EPEC+C.jejuni 1 subject, C.jejuni+EPEC+EIEC 1 subject and C.jejuni+EPEC+ETEC 1 subject. Conclusions: Most diarrhea occurs at the age of 1-3 years with good nutritional status of patients with low-medium family status. Approximately 48% of children with acute diarrhea excreted bacteria in their feces prooved by real-time PCR stool with the highest proportion is EPEC, followed by Campylobacter jejuni, EIEC and ETEC. ;Background: Diarrhea is still a public health problem in developing countries due to it?s morbidity and mortality. Diarrhea can be caused by viruses, bacteria and parasites. It is important to know the etiology to provide proper management, but there is currently no data on the bacteria that causes diarrhea in Indonesia. Objective: To characterize the clinical manifestations of children with acute diarrhea and determine the type of enteropathogens bacteria causing acute diarrhea using real-time PCR in Cipto Mangunkusumo Hospital. Methods: This was a cross-sectional study, done in June-November 2015. Stool specimens were collected from patients aged 1-15 years with acute diarrhea and tested for bacterial enteropathogens using real-time PCR. Results: Of the 60 children enrolled, mostly aged 1-3 years, good nutritional status, from low income families and secondary education mothers, most have not received antibiotics prior to hospital admission but had received oral rehydration fluids. The clinical features of acute diarrhea caused by bacterial infection is diarrhea frequency ≤5X / day without fecal leukocytosis and fat malabsorption. From 60 subjects, 29 (48,3%) children excreted bacteria in their feces prooved by real-time PCR. Distribution of pathogenic bacterial infection causes acute diarrhea by real-time PCR as follows: Campylobacter jejuni 7 subjects, pathogenic Escherichia coli 17 subjects which consists of EPEC 9 subjects, EIEC 5 subjects and ETEC 3 subjects. Multiple infections in subjects as follows: EPEC+EIEC 2 subjects, EPEC+C.jejuni 1 subject, C.jejuni+EPEC+EIEC 1 subject and C.jejuni+EPEC+ETEC 1 subject. Conclusions: Most diarrhea occurs at the age of 1-3 years with good nutritional status of patients with low-medium family status. Approximately 48% of children with acute diarrhea excreted bacteria in their feces prooved by real-time PCR stool with the highest proportion is EPEC, followed by Campylobacter jejuni, EIEC and ETEC.

Abstrak :
Latar belakang: Difteri merupakan penyakit infeksi bakteri yang diperantarai oleh toksin. Corynebacterium diphtheriae adalah penyebab tersering difteri. Diagnostik laboratorium harus dilakukan dengan cepat untuk menunjang diagnosis klinis difteri. Pemeriksaan mikroskopik tidak direkomendasikan karena tidak spesifik, kultur dan uji toksin yang merupakan uji baku emas cukup memakan waktu, membutuhkan keterampilan dan pengalaman serta hanya dilakukan di laboratorium rujukan. PCR merupakan metode pemeriksaan yang cepat, sensitif dan spesifik. Duplex real-time PCR dapat mendeteksi bakteri penyebab tersering dan gen pengkode toksin secara simultan. Tujuan penelitian: Melakukan optimasi uji duplex real time PCR untuk deteksi C. diphtheriae potensial toksigenik dan menerapkannya pada spesimen usap tenggorok pasien tersangka difteri. Metode: Duplex real-time PCR menggunakan dua pasang primer dan probe dengan target gen rpoB C.diphtheriae dan toksin difteri subunit A Tox. Parameter yang dioptimasi adalah suhu penempelan, konsentrasi masing-masing primer dan probe, inhibitor, reaksi silang dengan patogen lain dan ambang batas deteksi uji. Kemudian uji diaplikasikan pada spesimen usap tenggorok pasien tersangka difteri yang dirawat di RSPI Sulianti Saroso pada periode 2018-2019. Sebagai perbandingan dilakukan uji Elek untuk konfirmasi toksigenitas dan analisa data klinis pasien. Hasil: Kondisi optimal uji didapat pada suhu penempelan 55oC, konsentrasi primer Cd 0,4 μM, primer Tox 0,6 μM, probe Cd 0,5 μM dan probe Tox 0,625 μM, volume elusi ekstraksi DNA 50 μL, volume cetakan DNA 5 μL dan ambang batas deteksi 2 CFU/ml. Uji tidak bereaksi silang dengan mikroorganisme lain yang dicobakan. Dari 89 sampel, proporsi positif C.diphtheriae potensial toksigenik dengan uji duplex real-time PCR adalah 21,3%, sedangkan proporsi positif C.diphtheriae toksigenik menggunakan uji baku emas adalah 11,2%. Kesimpulan: Duplex real time PCR untuk deteksi C.diphtheriae potensial toksigenik telah dioptimasi dan diaplikasikan pada pasien tersangka difteri. Diharapkan uji ini dapat meningkatkan diagnosis laboratorium kasus difteri. ......Background: Diphtheria is toxin-mediated bacterial infection. The most common etiology is Corynebacterium diphtheriae. Laboratory diagnostic should be done immediately to support clinical diagnosis. Microscopic examination is not recommended, culture followed by toxin test is consider gold standard but timeconsuming, require experience and only done in referral laboratory. PCR is fast, sensitive and specific. Duplex real-time PCR can detect bacteria and toxin-encoding gene simultaneously. Objective: Optimizing duplex real-time PCR assay for detection of potentially toxigenic C.diphtheriae and applicate the assay on throat swab of suspected diphtheria patient. Method: Two pair of primers and specific probe targeting rpoB gene of C.diphtheriae and A-subunit of diphtheria toxin gene were used in this study. Parameters including annealling temperature, concentration of primers and probes, inhibitors, cross reaction and detection limit were being optimized to receive optimal condition. The optimized assay was applicated on throat swab of suspected diphtheria patient in Sulianti Saroso Infectious Disease Hospital at 2018-2019. Elek toxigenity test was used for comparison and clinical data of the patient were analyzed. Result: The optimum condition for duplex real-time PCR was received upon the annealing temperature 60oC, concentration of Cd primer 0,4 μM, Tox primer 0,6 μM, Cd probe 0,5 μM, Tox probe 0,625 μM, DNA elution volume 50 μL, DNA template volume 5 μL and detection limit 2 CFU/ml. There was no cross reaction found with other tested microorganisms. Of 89 samples, proportion of potentially toxigenic C.diphtheriae was 21,3% and proportion of toxigenic C.diphtheriae confirmed by gold standard was 11,2%. Conclusion: Duplex real time PCR has been optimized for detection of potentially toxigenic C.diphtheriae. This method can be used to detect C.diphtheriae and Tox simultaneosly and increase supporting diagnosis.

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ABSTRACT
Background: early detection of H. pylori is essential to prevent the development of infections into gastric malignancies. The coccoid form of H. pylori is difficult to detect either by culture or histopathology; however, it can be detected using molecular methods, such as real-time PCR. The study was expected to provide new information on the development of H. pylori detection. Methods: a cross-sectional study was conducted at the Gastrointestinal Endoscopy Center of Cipto Mangunkusumo Hospital between October 2016 and August 2017. The sampling method used was consecutive sampling. Biopsy from gastric antrum and corpus were performed in 64 patients. We collected 2 specimens from each site to be examined using real-time PCR and histopathology. Initially, we conducted real-time PCR optimization followed by application of clinical samples from gastric biopsy. Data analysis using McNemars χ2 and Kappa tests. Results: the real-time PCR showed 25% positivity, while the positive proportion of histopathological examination was 14%. Real-time PCR has a sensitivity and specificity 88.9% dan 85.5%, respectively. The McNemars x2 test showed that there is significantly different (p=0.039) between the two tests; kappa value (p=0.561). Conclusion: the real-time PCR examination is more sensitive than histopathology. This technique can improve diagnosis by 11% compared to histopathological examination.

Abstrak :
Latar Belakang: Penyakit Jantung Koroner merupakan penyebab utama kematian di dunia. Bakteri positif Gram dan negatif Gram telah sering diidentifikasi pada bakteremia dan disebut memiliki peran dalam penyakit vascular, termasuk Streptococcus sanguinis yang paling sering diisolasi dari pasien endokarditis dan sering dikaitkan dengan PJK.

Tujuan : Menganalisis jumlah Streptococcus sanguinis yang diisolasi dari plak gigi dan saliva subjek non-PJK dan PJK.

Metode : Koloni bakteri dari plak gigi dan saliva 16 subjek non-PJK dan 8 subjek PJK ditanam pada agar Mitis salivarius, diekstraksi DNA kemudian dikuantifikasi dengan teknik Real-Time PCR menggunakan primers spesifik 16S rRNA.

Hasil : Kuantifikasi Real-Time PCR menunjukkan perbedaan jumlah S. sanguinis antara subjek kelompok non-PJK dan PJK namun uji t tidak berpasangan menunjukkan perbedaannya tidak signifikan.

Kesimpulan : Pada subjek yang menjadi sampel penelitian ditemukan kecenderungan jumlah S. sanguinis asal plak gigi subjek PJK lebih tinggi dibandingkan subjek non-PJK dan jumlah S. sanguinis asal saliva subjek non-PJK cenderung lebih tinggi dibanding subjek PJK.

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Background : Coronary Heart Disease is the major cause of death in most countries in the world. Gram-positive and Gram-negative bacteria have been identified in bacteremia cases and said to have a role in various vascular disease, including Streptococcus sanguinis which is the most often bacteria to be isolated from endocarditis patients and often associated with CHD.

Objectives : To analyze the amount of Streptococcus sanguinis isolated from dental plaque and saliva of subjects with and without Coronary Heart Disease.

Methods : Bacterial colonies isolated from dental plaque and saliva of 16 subjects without CHD and 8 subjects with CHD are plated in Mitis salivarius agar, DNA are extracted and then quantified with Real-Time PCR technique using 16S rRNA primers.

Results : Real-Time PCR quantification shows that there’s a difference amount of S. sanguinis between the two groups of subjects but unpaired t-test shows that the differences are not statistically significant.

Conclusion : Subjects from this study shows tendency that the amount of S. sanguinis from dental plaque of CHD subjects is higher than non-CHD subjects and the amount of S. sanguinis from saliva of non-CHD subjects is higher than CHD subjects.

Abstrak :
ABSTRAK Multidrug-resistant tuberculosis (MDR-TB) adalah tuberkulosis yang disebabkan oleh galur Mtb yang resisten setidaknya terhadap rifampisin dan isoniazid (INH). Penelitian ini bertujuan menilai kemampuan AccuPower TB and MDR Real-Time PCR Kit sebagai metode alternatif dalam mendeteksi Mtb serta resistensi terhadap isoniazid dan rifampisin dibandingkan dengan metode kultur dan uji resistensi konvensional. Subjek penelitian terdiri dari 61 pasien tersangka MDR-TB. Sampel sputum dari semua subjek dilakukan pemeriksaan untuk Mtb dan resistensi terhadap INH dan rifampisin dengan Accupower TB and MDR Real-Time PCR Kit dan metode konvensional. 28 dari 52 pasien terdeteksi resisten terhadap INH dan rifampisin. 1 subjek terdeteksi hanya resisten terhadap INH. 1 subjek terdeteksi hanya resisten terhadap rifampisin. Sensitivitas dan PPV kit dalam mendeteksi Mtb diperoleh 98,1% dan 86,7%. Sensitivitas, spesifisitas, PPV, dan NPV kit dalam mendeteksi resistensi Mtb terhadap INH diperoleh 62,1%, 86,9%, 85,7%, dan 64,5%. Sensitivitas, spesifisitas, PPV, dan NPV kit dalam mendeteksi resistensi Mtb terhadap Rifampisin diperoleh 93,1%, 86,9%, 90% dan 90,9%. Accupower TB and MDR Real-Time PCR Kit dalam mendeteksi resistensi ganda Mtb terhadap INH dan Rifampisin (MDR-TB) memperoleh sensitivitas 53,8%, spesifisitas 57,1%, PPV 88,9%, dan NPV 64,7%. Kit ini cukup baik dalam mendeteksi Mtb dan resistensi terhadap rifampisin, tetapi kurang baik untuk mendeteksi resistensi terhadap INH. Deteksi adanya resistensi tunggal diperlukan, karena monoresistensi dapat berkembang menjadi multi-drug dan extended-drug resistant.

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ABSTRACT Multidrug-resistant tuberculosis (MDR-TB) is caused by mycobacterium that is resistant at least to rifampicin and isoniazid (INH). The aim of this study was to assess the performance of Accupower TB and MDR Real-Time PCR Kit compared to the conventional culture-based drug susceptibility test for Mycobacterium tuberculosis (Mtb). Subject was consisted of 61 patients who were suspected of MDR-TB. Sputum samples from the participants were tested for Mtb and INH and rifampicin resistance by Accupower TB and MDR Real-Time PCR Kit and conventional method. 28 of 52 patients were detected resistance to both INH and rifampicin. 1 subject was detected INH resistance only. 1 subject was detected rifampicin resistance only. Sensitivity and PPV of the kit to detect Mtb were 98,1% and 86,7%, respectively. Sensitivity, specificity, PPV, and NPV of the kit in detecting INH resistance were 62,1%, 86,9%, 85,7%, and 64,5%, respectively. Sensitivity, specificity, PPV, and NPV of the kit in detecting rifampicin resistance were 93,1%, 86,9%, 90%, and 90,9%, respectively. Sensitivity, specificity, PPV, and NPV of the kit in detecting INH and rifampicin resistance (MDR-TB) were 53,8%, 57,1%, 88,9%, and 64,7%, respectively. This kit was good enough to detect Mtb and Rifampisin resistance, but not good to detect INH resistance. Detection of single drug resistance is required as mono resistance might develop further to multi-drug and extended-drug resistant.